This paper presents an energy storage system based on ultra-capacitor to absorbing the regenerating energy of urban rail transit and releasing the energy when the train starts, which can cut down the energy waste. A modular power conversation scheme is proposed to accommodate the application of different electric supply system, with several module connected in series to endure high supply voltage. Multiphase power conversion circuit is adopted to share the high current, and a dual-loop control system is proposed to realize the bi-directional energy flow and achieve input voltage equalization in series modules. A voltage equalizer scheme is also introduced to guarantee that the ultra-capacitor works reliable and efficient, which consists of equalizer for cells in groups and voltage equalizer between the groups. At last, a small-scale prototype is build and the experiment results validate the feasibility of power conversion strategy.